Dear Gino, *Sometimes* ignoring the strict B-factor police is a valid option. Much of the time, it comes to building in weaker density vs not building, and it is a subjective call. I bet if you removed all weaker-density loops, your average B-factor would decrease, but you probably would have gained nothing, and not improved your model at all (you would probably make it worse, actually). And as Pavel pointed out, at >3 Angstroms, Wilson values are not so accurate. I would also look at phenix.polygon results. By the way, I have a related question for Pavel. When you guys were culling the PDB for structures, was there any attention paid to correct the ones that have residual B-factors in the PDB file? (Urzhumtseva, 2009 is not clear on this) I have found that a structure which was refined by refmac and deposited in 2005, where the residual B-factors are in the B column. This used to be a fairly common practice, before it was (thankfully!) settled by PDB that the B column should contain the full B factor (the way Phenix outputs by default). I still sometimes read articles where people report an average B-factor of 8 for a 2.2 Angstrom structure, and I know what is going on! I am asking this, because a few structures I solved recently to ~2 Angstrom resolution were all closer to the upper range of observed structures according to POLYGON, so I thought this could possibly be one reason. Engin On 4/21/10 10:42 AM, Gino Cingolani wrote:
Hi all,
we've solved a large structure (~20,000 residues/asymm unit), with 4-fold ncs and diffraction data to 3.3A.
The Rfree/Rfac is ~28%-24% with OK geometry with no major outliers in the Ramachandran plot. I would think I'm done (.. after 6 years!).
However, my refined model b-factor (~130A2) is>> Wilson b-factor (~80A2). Obviously I'm not too happy with it.
Here is what I tried to resolve this discrepancy: --> play with wxu_scale --> play with B-factor weight in ncs restraint (4-fold ncs) --> play with number of macrocycles --> Redefine tls groups
So far nothing really works, except switching from individual_adp to group_adp. However, this increases my Rfree by almost 3%.
Any ideas?
Thanks in advance,
Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry& Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111